Chem Biol Interact, 2003 Feb 1, 143-144, 325 - 32 Aldo-keto reductases as modulators of stress response; Chang Q et al.; Human aldose reductase (AKR1B1) has been implicated as a factor in the pathogenesis of diabetic complications . However, little is known about the physiological role of this enzyme or of related aldo-keto reductases in human tissues . In mammalian systems, a gene knock out approach is often employed as an experimental strategy to probe for gene function . However, in the murine system, phenotypic characterization of an aldose reductase (AKR1B3) knock out is likely to be complicated due to functional compensation by redundant AKRs including AKRs 1A (aldehyde reductase), 1B7 (FR-1) and 1B8 (MVDP) . As an alternate strategy, we are examining the budding yeast Saccharomyces cerevisiae as a model system for a functional genomics study of AKRs . A distinct advantage of this system centers on the ability to readily ablate multiple targeted genes in a single strain . In addition to providing insights into functional redundancy, this system allows us to use a genetic approach to study possible effector pathways associated with one or more individual genes . Yeast open reading frames (ORFs) encoding AKRs with functional similarity to human aldose reductase (AKR1B1) were identified by BLAST analysis and were functionally validated by studies of recombinant proteins . By ablating three of the yeast AKR genes most functionally similar to AKR1B1, we have created a unique strain of S . cerevisiae that shows enhanced sensitivity to stress . Ongoing studies with oligonucleotide arrays show that the triple null strain has an altered transcription profile consistent with an enhanced stress response in comparison with the parental strain . These data indicate that AKR-null strains may provide new insights into signaling mechanisms involving this family of proteins. Pac Symp Biocomput . 2003;:65-76. Kernel Cox regression models for linking gene expression profiles to censored survival data; Li H et al.; In functional genomics, one important problem is to relate the microarray gene expression profiles to various clinical phenotypes from patients . The success has been demonstrated in molecular classification of cancer in which gene expression data serve as predictors and different types of cancer are the binary or multi-categorical outcome variable . However, there has been less research in linking gene expression profiles to other types of phenotypes, in particular, the censored survival data such as patients' overall survival or cancer relapse times . In the paper, we develop a kernel Cox regression model for relating gene expression profiles to censored phenotypes in the framework the penalization method in terms of function estimation in reproducing kernel Hilbert spaces . To circumvent the problem of censoring, we use the negative partial likelihood as a loss function in the estimation procedure . The functional combinations of the original gene expression data identified by the method are highly correlated with the patients' survival times and at the same time account for the variability in the gene expression levels . We apply our method to data sets from diffuse large B-cell lymphoma, lung adenocarcinoma and breast carcinoma studies to verify its effectiveness . The results from these analyses indicate that the proposed method works very well in identifying subgroups of patients with different risks of death or relapse and in predicting the risk of relapse or death based on the gene expression profiles measured from the tumor samples taken from the patients. Nat Biotechnol, 2003 Mar, 21(3), 302 - 7 Epub 2003 Feb 24. TIP, a T-cell factor identified using high-throughput screening increases survival in a graft-versus-host disease model; Fiscella M et al.; A coordinated effort combining bioinformatic tools with high-throughput cell-based screening assays was implemented to identify novel factors involved in T-cell biology . We generated a unique library of cDNAs encoding predicted secreted and transmembrane domain-containing proteins generated by analyzing the Human Genome Sciences cDNA database with a combination of two algorithms that predict signal peptides . Supernatants from mammalian cells transiently transfected with this library were incubated with primary T cells and T-cell lines in several high-throughput assays . Here we describe the discovery of a T cell factor, TIP (T cell immunomodulatory protein), which does not show any homology to proteins with known function . Treatment of primary human and murine T cells with TIP in vitro resulted in the secretion of IFN-gamma, TNF-alpha, and IL-10, whereas in vivo TIP had a protective effect in a mouse acute graft-versus-host disease (GVHD) model . Therefore, combining functional genomics with high-throughput cell-based screening is a valuable and efficient approach to identifying immunomodulatory activities for novel proteins. Nat Biotechnol, 2003 Mar, 21(3), 294 - 301 Epub 2003 Feb 24. An integrated functional genomics screening program reveals a role for BMP-9 in glucose homeostasis; Chen C et al.; A coordinated functional genomics program was implemented to identify secreted polypeptides with therapeutic applications in the treatment of diabetes . Secreted factors were predicted from a diverse expressed-sequence tags (EST) database, representing >1,000 cDNA libraries, using a combination of bioinformatic algorithms . Subsequently, approximately 8,000 human proteins were screened in high-throughput cell-based assays designed to monitor key physiological transitions known to be centrally involved in the physiology of type 2 diabetes . Bone morphogenetic protein-9 (BMP-9) gave a positive response in two independent assays: reducing phosphoenolpyruvate carboxykinase (PEPCK) expression in hepatocytes and activating Akt kinase in differentiated myotubes . Purified recombinant BMP-9 potently inhibited hepatic glucose production and activated expression of key enzymes of lipid metabolism . In freely fed diabetic mice, a single subcutaneous injection of BMP-9 reduced glycemia to near-normal levels, with maximal reduction observed 30 hours after treatment . BMP-9 represents the first hepatic factor shown to regulate blood glucose concentration . Using a combination of bioinformatic and high-throughput functional analyses, we have identified a factor that may be exploited for the treatment of diabetes. Curr Opin Mol Ther, 2002 Dec, 4(6), 572 - 6 From genomics to cancer vaccines: patient-tailored or universal vaccines? Nadler LM, Schultze JL. There is little doubt about the existence of tumor-associated antigens and T-cell-mediated immune responses against cancer antigens . Antitumor immunity has been identified in many patients with very different types of cancer . Nevertheless, there is still no consensus regarding the correct targets to be used for cancer immunotherapy, including cancer vaccines and adoptive T-cell transfer of tumor antigen-specific T-cells . Certainly, functional genomics and proteomics will have implications on the field of tumor antigen discovery due to the possibility of molecular characterization of whole transcriptomes and proteomes of cancer cells, thereby also identifying potential new targets for cancer immunotherapy . Based on fundamental immunological knowledge, it is hypothesized that the most promising approach would be patient-tailored . Alternatively, if genes are identified in the majority of all cancers, a more universal approach to cancer vaccines can be envisioned . Success with these opposing strategies will greatly rely on whether it is possible to induce robust immunity against the antigens identified, whether technical and regulatory issues of patient-tailored approaches can be adequately addressed, and certainly also which approach will be economically more advantageous. Bioessays, 2003 Mar, 25(3), 266 - 73 Statistical bioinformatic methods in microbial genome analysis; Lio P; It is probable that, increasingly, genome investigations are going to be based on statistical formalization . This review summarizes the state of art and potentiality of using statistics in microbial genome analysis . First, I focus on recent advances in functional genomics, such as finding genes and operons, identifying gene conversion events, detecting DNA replication origins and analysing regulatory sites . Then I describe how to use phylogenetic methods in genome analysis and methods for genome-wide scanning for positively selected amino acids . I conclude with speculations on the future course of genome statistical modeling . Swiss Med Wkly, 2003 Jan 25, 133(3-4), 31 - 8 Functional genomics and gene microarrays--the use in research and clinical medicine; Joos L et al.; In the year 2000, the Human Genome Project Consortium presented the first complete draft of the human genome together with Celera Genetics . Since then, the so-called "post-genome era" has started . Microarrays are capable of profiling gene expression patterns of tens of thousands of genes in a single experiment and thus allow a systematic analysis of DNA and RNA variation . They seem likely to become a standard tool of both molecular biology research and clinical diagnostics . These prospects have attracted great interest and investment from both the public and private sectors . This review introduces the principle of microarray technology and gives an overview of its current and future potential in clinical medicine. J Biol Chem, 2003 May 2, 278(18), 15951 - 7 Epub 2003 Feb 17. Bone-related genes expressed in advanced malignancies induce invasion and metastasis in a genetically defined human cancer model; Rich JN et al.; We employed a genetically defined human cancer model to investigate the contributions of two genes up-regulated in several cancers to phenotypic changes associated with late stages of tumorigenesis . Specifically, tumor cells expressing two structurally unrelated bone-related genes, osteonectin and osteoactivin, acquired a highly invasive phenotype when implanted intracranially in immunocompromised mice . Mimicking a subset of gliomas, tumor cells invaded brain along blood vessels and developed altered vasculature at the brain-tumor interface, suggesting that production of those two proteins by tumor cells may create a complex relationship between invading tumor and vasculature co-opted during tumor invasion . Interestingly, the same tumor cells formed massive spontaneous metastases when implanted subcutaneously . This dramatic alteration in tumor phenotype indicates that cellular microenvironment plays an important role in defining the specific effects of those gene products in tumor behavior . In vitro examination of tumor cells expressing either osteonectin or osteoactivin revealed that there was no impact on cellular growth or death but increased invasiveness and expression of MMP-9 and MMP-3 . Specific pharmacologic inhibitors of MMP-2/9 and MMP-3 blocked the increased in vitro invasion associated with osteoactivin expression, but only MMP-3 inhibition altered the invasive in vitro phenotype mediated by osteonectin . Results from this genetically defined model system are supported by similar findings obtained from several established tumor cell lines derived originally from human patients . In sum, these results reveal that the expression of a single bone-related gene can dramatically alter or modify tumor cell behavior and may confer differential growth characteristics in different microenvironments . Genetically defined human cancer models offer useful tools in functional genomics to define the roles of specific genes in late stages of carcinogenesis. Phytochemistry, 2003 Mar, 62(6), 817 - 36 Plant metabolomics: large-scale phytochemistry in the functional genomics era; Sumner LW et al.; Metabolomics or the large-scale phytochemical analysis of plants is reviewed in relation to functional genomics and systems biology . A historical account of the introduction and evolution of metabolite profiling into today's modern comprehensive metabolomics approach is provided . Many of the technologies used in metabolomics, including optical spectroscopy, nuclear magnetic resonance, and mass spectrometry are surveyed . The critical role of bioinformatics and various methods of data visualization are summarized and the future role of metabolomics in plant science assessed. Mol Genet Genomics, 2003 Feb, 268(5), 675 - 83 Epub 2003 Jan 15. Deletion of Aspergillus nidulans aroC using a novel blaster module that combines ET cloning and marker rescue; Krappmann S et al.; Blaster cassettes are of significant value in functional genomics, as they represent tools with which to inactivate duplicated or homologous genes in an individual organism . We have constructed a novel blaster module which allows repeated gene deletion in the filamentous fungus Aspergillus nidulans . Because bacterial resistance marker cassettes are employed as flanking repeats in direct orientation, the blaster cassette is suited for recombinogenic engineering by ET cloning in Escherichia coli . The functionality of the blaster module was demonstrated by deleting the chorismate mutase-encoding gene aroC of A . nidulans, followed by marker rescue based on mitotic recombination . The resulting aroCDelta strains are auxotrophic for phenylalanine but not tyrosine, and display a limited capacity for fruit body formation and ascosporogenesis, which depends on the phenylalanine/tyrosine supply . The data support the notion that amino acid status has a strong impact on cleistothecium development in A . nidulans. Pest Manag Sci, 2003 Feb, 59(2), 143 - 8 A genomics approach to crop pest and disease research; Keon J et al.; Genome-wide analyses of gene function and gene expression are beginning to yield valuable information in many areas of biological research, and these genomic tools are now being applied to crop pest and disease research . DNA sequencing of cDNA libraries to generate sets of expressed sequence tags (ESTs) are allowing gene compendiums for crop diseases to be compiled . Annotation of such data collections is also providing a wealth of functional information about gene products through similarities to proteins with known function . The next phase of the functional genomics era will be to employ large-scale techniques to knock out or silence genes in order to synthesize gene-specific mutants for phenotypic analysis and to use micro-array methodology to analyze global gene expression, protein turnover and protein processing during the processes of parasitism and colonization . Application of these technologies promises to accelerate the pace that biological information relevant to crop protection accrues . The ability of researchers to assimilate this information into complex models and workable hypotheses is, thus, set to revolutionize the way we study pests and diseases of crop plants. Org Lett, 2003 Feb 20, 5(4), 383 - 5 Synthesis of nucleoside dimers bridged on ribose with a butadiynyl group; Jung F et al.; {reaction: see text} The nucleoside dimer linked by a butadiynediyl group at C-3'beta may serve as a building block for the preparation of backbone-modified oligonucleotides for DNA repair or mutation in functional genomics . We prepared this type of dimer by an Eglington or Sonogashira coupling reaction . The unsymmetrical dimer was synthesized by coupling the acetylene with the bromoacetylene . Only marginal cytotoxicity was detected for one of the dimers. Curr Opin Allergy Clin Immunol, 2002 Oct, 2(5), 389 - 93 Genetics of IL-13 and functional relevance of IL-13 variants; Vercelli D; Studies in both humans and mice clearly show that interleukin (IL)-13 is a central regulator of allergic inflammation . Numerous single nucleotide polymorphisms have been recently identified in the IL-13 gene and have been found to be associated with allergic and/or asthmatic phenotypes in different populations throughout the world . Furthermore, functional genomics studies are highlighting mechanistic pathways that may link genetic variation in IL-13 and disease . IL-13 is therefore an ideal model to study the impact of genetic variation on the regulation of gene expression and function in complex diseases. Drug Discov Today, 2003 Feb 15, 8(4), 168 - 74 Fulfilling the promise: drug discovery in the post-genomic era; Chanda SK et al.; The genomic era has brought with it a basic change in experimentation, enabling researchers to look more comprehensively at biological systems . The sequencing of the human genome coupled with advances in automation and parallelization technologies have afforded a fundamental transformation in the drug target discovery paradigm, towards systematic whole genome and proteome analyses . In conjunction with novel proteomic techniques, genome-wide annotation of function in cellular models is possible . Overlaying data derived from whole genome sequence, expression and functional analysis will facilitate the identification of causal genes in disease and significantly streamline the target validation process . Moreover, several parallel technological advances in small molecule screening have resulted in the development of expeditious and powerful platforms for elucidating inhibitors of protein or pathway function . Conversely, high-throughput and automated systems are currently being used to identify targets of orphan small molecules . The consolidation of these emerging functional genomics and drug discovery technologies promises to reap the fruits of the genomic revolution. Curr Top Med Chem, 2003, 3(6), 659 - 85 Supertargeted chemistry: identifying relationships between molecular structures and their sub-cellular distribution; Rosania GR; Supertargeted chemistry is the study of how chemical structures localize or direct molecules to specific sub-cellular compartments in living cells . Supertargeting can be used to increase the activity or specificity of an inhibitor against its target, by concentrating the inhibitor in the particular organelle where the target is active . But, unlike structure-activity relationships, structure-localization relationships are not a simple function of compound concentration . Various aspects of mitochondrial physiology, proteomics and pharmacology have made this the organelle of choice for supertargeting studies . While exploration of supertargeting strategies to this and the other organelles has been limited, combinatorial chemical libraries of fluorescent molecules are beginning to illuminate new supertargeting mechanisms at the sub-cellular level . Moreover, predictive approaches that determine the relationship between a molecule's features and sub-cellular localization are being developed in the related field of functional genomics . Applied to the small molecules, such strategies could prove useful for predicting structure-localization relationships amongst large libraries of compounds. Genome Res, 2003 Feb, 13(2), 264 - 71 Systematic discovery of new genes in the Saccharomyces cerevisiae genome; Kessler MM et al.; We used genome-wide comparative analysis of predicted protein sequences to identify many novel small genes, named smORFs for small open reading frames, within the budding yeast genome . Further analysis of 117 of these new genes showed that 84 are transcribed . We extended our analysis of one smORF conserved from yeast to human . This investigation provides an updated and comprehensive annotation of the yeast genome, validates additional concepts in the study of genomes in silico, and increases the expected numbers of coding sequences in a genome with the corresponding impact on future functional genomics and proteomics studies. Proc Natl Acad Sci U S A, 2003 Feb 18, 100(4), 1844 - 8 Epub 2003 Jan 27. A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA; Tiscornia G et al.; We describe the use of lentiviral vectors expressing small interfering RNAs (siRNAs) to knock down the expression of specific genes in vitro and in vivo . A lentiviral vector capable of generating siRNA specific for GFP after transduction of 293T-GFP cell lines showed no GFP fluorescence . Furthermore, no GFP-specific RNA could be detected . When eggs from GFP-positive transgenic mice were transduced with lentivirus-expressing siGFP virus, reduced fluorescence could be seen in blastocysts . More interestingly, pups from F(1) progeny, which expressed siGFP, showed considerably diminished fluorescence and decreased GFP . We propose that an approach of combining transgenesis by lentiviral vectors expressing siRNAs can be used successfully to generate a large number of mice in which the expression of a specific gene(s) can be down-regulated substantially . We believe that this approach of generating "knockdown" mice will aid in functional genomics. Proc Natl Acad Sci U S A, 2003 Feb 4, 100(3), 1004 - 9 Epub 2003 Jan 27. Molecular features of adult mouse small intestinal epithelial progenitors; Stappenbeck TS et al.; The adult mouse small intestinal epithelium undergoes perpetual regeneration, fueled by a population of multipotential stem cells and oligopotential daughters located at the base of crypts of Lieberkuhn . Although the morphologic features of small intestinal epithelial progenitors (SiEPs) are known, their molecular features are poorly defined . Previous impediments to purification and molecular characterization of SiEPs include lack of ex vivo clonigenic assays and the difficulty of physically retrieving them from their niche where they are interspersed between their numerous differentiated Paneth cell daughters . To overcome these obstacles, we used germ-free transgenic mice lacking Paneth cells to obtain a consolidated population of SiEPs with normal proliferative activity . These cells were harvested by laser capture microdissection . Functional genomics analysis identified 163 transcripts enriched in SiEPs compared with Paneth cell-dominated normal crypt base epithelium . The dataset was validated by (i) correlation with the organellar composition of SiEPs versus Paneth cells, (ii) similarities to databases generated from recent mouse hematopoietic and neural stem cell genome anatomy projects, and (iii) laser capture microdissectionreal-time quantitative RT-PCR studies of progenitor cell-containing populations retrieved from the small intestines, colons, and stomachs of conventionally raised mice . The SiEP profile has prominent representation of genes involved in c-myc signaling and in the processing, localization, and translation of mRNAs . This dataset, together with our recent analysis of gene expression in the gastric stem cell niche, discloses a set of molecular features shared by adult mouse gut epithelial progenitors. Eur J Pharm Biopharm, 2003 Jan, 55(1), 3 - 10 Pharmaceutical biotechnology products approved within the European Union; Walsh G; The manufacture of therapeutic proteins represented the first true industrial application of recombinant DNA technology . Thus far some 88 recombinant proteins/monoclonal antibody-based products have gained marketing approval within the European Union (EU) . This represents 36% of all new drug approvals since the introduction of the new centralized European drug approval system in 1995 . More recently, an increasing proportion of approved proteins are engineered, tailored to display altered pharmacokinetic profiles or reduced immunogenicity in man . Currently no nucleic acid-based products are approved in the EU . Technical innovations/milestones likely characterizing the biopharmaceutical industry within the next decade include approval of some products produced in transgenic systems, approval of some products administered by non-parenteral means, approval of at least some nucleic acid-based products and the identification of novel biopharmaceuticals/biopharmaceutical targets through discoveries in functional genomics and proteomics. Curr Opin Chem Biol, 2003 Feb, 7(1), 97 - 102 Functional genomics of intracellular peptide recognition domains with combinatorial biology methods; Sidhu SS et al.; Phage-displayed peptide libraries have been used to identify specific ligands for peptide-binding domains that mediate intracellular protein-protein interactions . These studies have provided significant insights into the specificities of particular domains . For PDZ domains that recognize C-terminal sequences, the information has proven useful in identifying natural binding partners from genomic databases . For SH3 domains that recognize internal proline-rich motifs, the results of database searches with phage-derived ligands have been compared with the results of yeast-two-hybrid experiments to produce overlap networks that reliably predict natural protein-protein interactions . In addition, libraries of phage-displayed PDZ and SH3 domains have been used to identify the residues responsible for ligand recognition, and also to engineer domains with altered specificities. Drug Discov Today, 2002 Sep 15, 7(18 Suppl), S125 - 30 High-throughput cell-based assays in yeast; Tucker CL; With the sequencing of many genomes now completed, biologists are faced with the challenge of deciphering the function and association of an immense number of predicted proteins . Comprehension of the networks of proteins and chemicals that comprise the cells and tissues of an organism, and the specific roles of proteins in these networks, will be a necessary next step to understanding cellular function in healthy and diseased states . In the past decade, the budding yeast Saccharomyces cerevisiae has emerged as an important tool for large-scale functional genomics analyses . This review describes the use of yeast cell-based assays in the post-genomic era, focusing on high-throughput functional genomics and drug discovery. Genet Med, 2002 Nov-Dec, 4(6 Suppl), 62S - 65S Bioinformatics and genomic medicine; Kim JH; Bioinformatics is a rapidly emerging field of biomedical research . A flood of large-scale genomic and postgenomic data means that many of the challenges in biomedical research are now challenges in computational science . Clinical informatics has long developed methodologies to improve biomedical research and clinical care by integrating experimental and clinical information systems . The informatics revolution in both bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics, and prognostics . Postgenome informatics, powered by high-throughput technologies and genomic-scale databases, is likely to transform our biomedical understanding forever, in much the same way that biochemistry did a generation ago . This paper describes how these technologies will impact biomedical research and clinical care, emphasizing recent advances in biochip-based functional genomics and proteomics . Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine-learning algorithms are discussed . Use of integrative biochip informatics technologies, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and the integrated management of biomolecular databases, are also discussed. In Silico Biol, 2002, 2(3), 249 - 55 Finding and decrypting of promoters contributes to the elucidation of gene function; Werner T; The combination of full-scale genomic sequencing with high throughput expression analysis provides a new and largely unexploited basis for in silico functional genomics . Recent break through developments in locating and analyzing promoters now allow extending functional genomics in silico far beyond identification of protein sequences into the complex regulatory structures and mechanisms of the genome . However, only first examples of this new type of approach are emerging at present and intensive further developments of bioinformatics tools will be required before such analysis can become large-scale routine in genomic sequence analysis . Nevertheless, the door to a new dimension of functional analysis of the genomic sequence is open . Finally, only the tight integration of the enormous amount of knowledge gained from proteins sequence analysis with the complementary information about gene regulation will afford us with a more complete picture of the networks than constitute life. Genome Biol . 2003;4(1):201 . Epub 2003 Jan 03. Post-genomic insights into plant nodulation symbioses; Gresshoff PM; Several legume genes involved in establishing nitrogen fixation have been discovered using functional genomics; when mutated, the genes affect symbioses, and all encode receptor kinases . This provides long-awaited insights into a complex plant-bacterium interaction and heralds the possibility of extending the range of plants susceptible to nitrogen-fixing nodulation. Expert Opin Ther Targets, 2001 Jun, 5(3), 297 - 301 Target validation and functional analyses using antisense oligonucleotides; Taylor MF; The human genome project (HGP) has been described as the single most important project in biology and the biomedical sciences to date . In February 2001, the efforts of the HGP resulted in the publication of a 'working draft' of the entire human genome and it is expected that final sequencing and annotation of the genome will be completed by 2003 . Researchers are now focusing efforts on the identification of the function of the reported 30,000 human genes . During the past few years, antisense oligomers have been widely used as potent tools for functional genomics and drug target validation . This article describes the emerging and established antisense technologies that will be used to continue the efforts to unlock the function of the human genome and to discover novel drug targets for the treatment of human diseases. Novartis Found Symp, 2002, 247, 91 - 101; discussion 101-3, 119-28, 244-52 The KEGG database; Kanehisa M; KEGG is a suite of databases and associated software for understanding and simulating higher-order functional behaviours of the cell or the organism from its genome information . First, KEGG computerizes data and knowledge on protein interaction networks (PATHWAY database) and chemical reactions (LIGAND database) that are responsible for various cellular processes . Second, KEGG attempts to reconstruct protein interaction networks for all organisms whose genomes are completely sequenced (GENES and SSDB databases) . Third, KEGG can be utilized as reference knowledge for functional genomics (EXPRESSION database) and proteomics (BRITE database) experiments . I will review the current status of KEGG and report on new developments in graph representation and graph computations. Bioinformatics, 2003 Jan 22, 19(2), 241 - 8 Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO); Yeh I et al.; MOTIVATION: A critical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge . The Gene Ontology (GO; provides a taxonomy of concepts and their attributes for annotating gene products . As GO increases in size, its ongoing construction and maintenance becomes more challenging . In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protege-2000, to the maintenance and development of GO . RESULTS: We transferred GO to Protege-2000 in order to evaluate its suitability for GO . The graphical user interface supported browsing and editing of GO . Tools for consistency checking identified minor inconsistencies in GO and opportunities to reduce redundancy in its representation . The Protege Axiom Language proved useful for checking ontological consistency . The PROMPT tool allowed us to track changes to GO . Using Protege-2000, we tested our ability to make changes and extensions to GO to refine the semantics of attributes and classify more concepts . AVAILABILITY: Gene Ontology in Protege-2000 and the associated code are located at Protege-2000 is available from http://protege.stanford.edu. Ann N Y Acad Sci, 2002 Dec, 975, 180 - 91 A functional genomics approach to Kaposi's sarcoma; Moses AV et al.; Kaposi's sarcoma (KS) is the most frequent malignancy afflicting acquired immune-deficiency syndrome (AIDS) patients . Tumor lesions are characterized by spindle cells of vascular origin and vascularization . Kaposi's sarcoma-associated herpes virus (KSHV) is consistently found in all forms of KS . Infection of dermal microvascular endothelial cells (DMVEC) with KSHV recapitulates spindle cell formation in vitro . We studied this transformation process by DNA microarray analysis comparing the RNA expression profiles of KSHV-infected and mock-infected DMVEC . Genes involved in tumorigenesis, angiogenesis, host defense, cell growth and differentiation, transcription, and metabolism were observed to change significantly upon infection with KSHV . One of the most consistently KSHV-induced genes was the receptor tyrosine kinase and proto-oncogene c-Kit . Inhibition of c-Kit activity with the pharmacological inhibitor of c-Kit signaling STI571 reversed the KSHV-induced morphological transformation of DMVEC . Moreover, overexpression studies showed that c-Kit was sufficient to induce spindle cell formation (Moses et al . J . Virol . 76(16): 8383-8399) . These data demonstrate that microarrays are useful for the identification of pharmacological targets essential for KS tumorigenesis. Ann N Y Acad Sci, 2002 Dec, 975, 160 - 8 Unlocking the mysteries of virus-host interactions: does functional genomics hold the key? Korth MJ, Katze MG. The interactions between viruses and the cells they infect are complex and multifaceted . While viruses strive to usurp cellular functions to their advantage, the cell strives to thwart these efforts by mounting a variety of defensive responses . These responses may include the induction of interferon, stress response, or apoptotic pathways, all of which are accompanied by changes in gene expression . Some viruses consistently win this tug of war, whereas others succumb to cellular defense mechanisms . The viral and cellular factors that determine the outcome are for the most part still unknown . With the advent of functional genomics, potent new technologies are now available to probe the complexities of virus-host interactions in ever increasing depth and detail . We describe here our efforts to use microarrays, proteomics, and bioinformatics to focus in on the changes in gene expression and protein production that occur in a virus-infected cell and to use these technologies to unlock the mysteries of virus-host interactions. Genome Biol . 2002;3(12):RESEARCH0080 . Epub 2002 Dec 23. A Drosophila full-length cDNA resource; Stapleton M et al.; BACKGROUND: A collection of sequenced full-length cDNAs is an important resource both for functional genomics studies and for the determination of the intron-exon structure of genes . Providing this resource to the Drosophila melanogaster research community has been a long-term goal of the Berkeley Drosophila Genome Project . We have previously described the Drosophila Gene Collection (DGC), a set of putative full-length cDNAs that was produced by generating and analyzing over 250,000 expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages . RESULTS: We have generated high-quality full-insert sequence for 8,921 clones in the DGC . We compared the sequence of these clones to the annotated Release 3 genomic sequence, and identified more than 5,300 cDNAs that contain a complete and accurate protein-coding sequence . This corresponds to at least one splice form for 40% of the predicted D . melanogaster genes . We also identified potential new cases of RNA editing . CONCLUSIONS: We show that comparison of cDNA sequences to a high-quality annotated genomic sequence is an effective approach to identifying and eliminating defective clones from a cDNA collection and ensure its utility for experimentation . Clones were eliminated either because they carry single nucleotide discrepancies, which most probably result from reverse transcriptase errors, or because they are truncated and contain only part of the protein-coding sequence. Genome Biol . 2002;3(12):RESEARCH0069 . Epub 2002 Nov 25. Supervised clustering of genes; Dettling M et al.; BACKGROUND: We focus on microarray data where experiments monitor gene expression in different tissues and where each experiment is equipped with an additional response variable such as a cancer type . Although the number of measured genes is in the thousands, it is assumed that only a few marker components of gene subsets determine the type of a tissue . Here we present a new method for finding such groups of genes by directly incorporating the response variables into the grouping process, yielding a supervised clustering algorithm for genes . RESULTS: An empirical study on eight publicly available microarray datasets shows that our algorithm identifies gene clusters with excellent predictive potential, often superior to classification with state-of-the-art methods based on single genes . Permutation tests and bootstrapping provide evidence that the output is reasonably stable and more than a noise artifact . CONCLUSIONS: In contrast to other methods such as hierarchical clustering, our algorithm identifies several gene clusters whose expression levels clearly distinguish the different tissue types . The identification of such gene clusters is potentially useful for medical diagnostics and may at the same time reveal insights into functional genomics. Mamm Genome, 2003 Jan, 14(1), 65 - 70 Generation and sequence characterization of a normalized cDNA library from swine ovarian follicles; Caetano AR et al.; Ovulation rate is a major factor determining litter size in swine and is, therefore, a trait of economic importance to the pork industry . The dynamics of follicle development, which in turn are dictated by a balance between follicle recruitment, maturation, selection, and atresia, are a major determining factor of ovulation rate . The role of several genes expressed in the ovaries during these processes has been described, but studies utilizing large-scale genomic approaches have yet to be conducted to examine gene expression in this tissue more globally . We have developed a normalized cDNA library from swine ovarian follicles in various stages of development, ranging from 2.0 to 10.0 mm in diameter, collected from gilts from divergent genetic lines selected for high and low ovulation rates, during the 7 initial days of the follicular phase of the estrous cycle . EST sequences were obtained from 5231 distinct clones derived from this library . In total, 3479 unique sequence clusters were obtained, of which 2661 singletons (76.5%) were observed . BLASTN searches with the primary sequences from the clusters obtained resulted in 1037 sequences not matching (E <1.0(-06) any of the sequences in the nt database (29.8% novelty rate) . This resource will facilitate the use of cDNA microarrays in functional genomics studies aiming at unraveling the genetic and physiological mechanisms underlying follicle maturation and ovulation rate in swine. Drugs Today (Barc), 2002 Apr, 38(4), 235 - 44 Strategies to identify disease genes; Ashton GH et al.; The correlation between genes and disease began in earnest in the early 1900s with the identification of Mendelian-like inheritance of "inborn errors of metabolism." Since then, the ever-broadening field of genetics has been established as one of the most important and groundbreaking branches of science and medicine to date . With the announcement of a "working draft" sequence of the human genome in 2001, the vast array of both genomic and expressed sequence information available in the public databases alone has meant that the concept of hunting for genes is evolving . Nowadays, researchers can substitute many labor-intensive hours in the lab for less time searching on the World Wide Web . Specialization within genetics has been continuously providing subsets of the genre such as genomics, pharmacogenetics, chemogenomics, gene therapy, proteomics and functional genomics, all of which are based on the fundamental starting block, the gene . This review aims to summarize both traditional and current strategies for identifying susceptibility and monogenetic disease genes and describes how these strategies have evolved in tune with the ever-expanding wealth of information now available at our fingertips. Anal Biochem, 2003 Jan 15, 312(2), 101 - 5 Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride; Raghavachari N et al.; Microarray technology is currently being used extensively in functional genomics research and modern drug discovery and development . Henceforward, tremendous application potential for this technology exists in the fields of clinical diagnostics and prognostics, pathology, and toxicology for high-throughput analysis of "disease" gene expression . However, the major hurdle now in this technology is not the performance of the arrays but rather the efficient reproducibility of the hybridization signal intensity in a fluorescence-based analysis . The sensitivity of fluorescence detection on an array is to a large extent limited by the amount of background signal arising due to nonspecifically bound probes and fluorescence that is intrinsically associated with the chip substrate and/or the attached target DNA, the so-called autofluorescence . Here, we describe a simple and efficient method to reduce autofluorescence from undetermined sources on coated glass slides with and without DNA arrays . This sodium borohydride-mediated reduction process resulted in significantly lower and more even background fluorescence . This in turn extended the dynamic range of detection and reduced the average coefficient of variation of fluorescent signal ratios on DNA microarrays in addition to improving the detection of genes that are expressed at a low level. Proc Natl Acad Sci U S A, 2003 Jan 21, 100(2), 605 - 10 Epub 2003 Jan 14. Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics; Mootha VK et al.; Identifying the genes responsible for human diseases requires combining information about gene position with clues about biological function . The recent availability of whole-genome data sets of RNA and protein expression provides powerful new sources of functional insight . Here we illustrate how such data sets can expedite disease-gene discovery, by using them to identify the gene causing Leigh syndrome, French-Canadian type (LSFC, Online Mendelian Inheritance in Man no . 220111), a human cytochrome c oxidase deficiency that maps to chromosome 2p16-21 . Using four public RNA expression data sets, we assigned to all human genes a "score" reflecting their similarity in RNA-expression profiles to known mitochondrial genes . Using a large survey of organellar proteomics, we similarly classified human genes according to the likelihood of their protein product being associated with the mitochondrion . By intersecting this information with the relevant genomic region, we identified a single clear candidate gene, LRPPRC . Resequencing identified two mutations on two independent haplotypes, providing definitive genetic proof that LRPPRC indeed causes LSFC . LRPPRC encodes an mRNA-binding protein likely involved with mtDNA transcript processing, suggesting an additional mechanism of mitochondrial pathophysiology . Similar strategies to integrate diverse genomic information can be applied likewise to other disease pathways and will become increasingly powerful with the growing wealth of diverse, functional genomics data. Annu Rev Med, 2003, 54, 371 - 92 Epub 2001 Dec 03. Functional genomic of the paraoxonase (PON1) polymorphisms: effects on pesticide sensitivity, cardiovascular disease, and drug metabolism; Costa LG et al.; This review focuses on the functional genomics of the human paraoxonase (PON1) polymorphisms . Levels and genetic variability of the PON1 position 192 isoforms (Gln/Arg) influence sensitivity to specific insecticides or nerve agents and risk for cardiovascular disease . A more recent area of investigation, the role of PON1 in drug metabolism, is also discussed . We emphasize the importance of considering both PON1 isoforms and PON1 levels in disease/sensitivity association studies. Nucleic Acids Res, 2003 Jan 1, 31(1), 452 - 5 The CATH database: an extended protein family resource for structural and functional genomics; Pearl FM et al.; The CATH database of protein domain structures currently contains 34 287 domain structures classified into 1383 superfamilies and 3285 sequence families . Each structural family is expanded with domain sequence relatives recruited from GenBank using a variety of efficient sequence search protocols and reliable thresholds . This extended resource, known as the CATH-protein family database (CATH-PFDB) contains a total of 310 000 domain sequences classified into 26 812 sequence families . New sequence search protocols have been designed, based on these intermediate sequence libraries, to allow more regular updating of the classification . Further developments include the adaptation of a recently developed method for rapid structure comparison, based on secondary structure matching, for domain boundary assignment . The philosophy behind CATHEDRAL is the recognition of recurrent folds already classified in CATH . Benchmarking of CATHEDRAL, using manually validated domain assignments, demonstrated that 43% of domains boundaries could be completely automatically assigned . This is an improvement on a previous consensus approach for which only 10-20% of domains could be reliably processed in a completely automated fashion . Since domain boundary assignment is a significant bottleneck in the classification of new structures, CATHEDRAL will also help to increase the frequency of CATH updates. Nucleic Acids Res, 2003 Jan 1, 31(1), 421 - 3 ARED 2.0: an update of AU-rich element mRNA database; Bakheet T et al.; The Adenylate Uridylate (AU)-Rich Element Database, ARED-mRNA version 2.0, contains information not present in the previous ARED . This includes additional data entries, new information and links to Unigene, LocusLink, RefSeq records and mouse homologue data . An ARE consensus sequence specific to the 3'UTR is the basis of ARED that demonstrated two important findings: (i) AREs are present in a large, previously unrecognized set of human mRNAs; and (ii) ARE-mRNAs encode proteins of diverse functions which are largely involved in early and transient biological responses . In this update, we have modified the strategy for identifying ARE-mRNA in order to systematically deal with inconsistencies of molecule type and mRNA region in GenBank records . Potential uses for the ARED in functional genomics are also given . The database is accessible via the web, with a new querying system that allows searching ARE-mRNAs by any public database identifier or name . The ARED website also contains relevant links to uses for the ARED. Nucleic Acids Res, 2003 Jan 1, 31(1), 342 - 4 The PlantsP and PlantsT Functional Genomics Databases; Tchieu JH et al.; PlantsP and PlantsT allow users to quickly gain a global understanding of plant phosphoproteins and plant membrane transporters, respectively, from evolutionary relationships to biochemical function as well as a deep understanding of the molecular biology of individual genes and their products . As one database with two functionally different web interfaces, PlantsP and PlantsT are curated plant-specific databases that combine sequence-derived information with experimental functional-genomics data . PlantsP focuses on proteins involved in the phosphorylation process (i.e., kinases and phosphatases), whereas PlantsT focuses on membrane transport proteins . Experimentally, PlantsP provides a resource for information on a collection of T-DNA insertion mutants (knockouts) in each kinase and phosphatase, primarily in Arabidopsis thaliana, and PlantsT uniquely combines experimental data regarding mineral composition (derived from inductively coupled plasma atomic emission spectroscopy) of mutant and wild-type strains . Both databases provide extensive information on motifs and domains, detailed information contributed by individual experts in their respective fields, and descriptive information drawn directly from the literature . The databases incorporate a unique user annotation and review feature aimed at acquiring expert annotation directly from the plant biology community . PlantsP is available at and PlantsT is available at http://plantst.sdsc.edu. Clin Oncol (R Coll Radiol), 2002 Dec, 14(6), 437 - 41 Late radiation morbidity in a patient with carcinoma of the cervix; Appel W et al.; The Grand Round was held at the Christie Hospital on the 26 November 2001 . It followed a talk by Professor Kate Vallis of the Princess Margaret Hospital in Toronto on, "A functional genomics approach to understanding normal issue response and ionizing radiation". Mol Endocrinol, 2003 Jan, 17(1), 27 - 41 Trapping and characterization of novel retinoid response elements; Glozak MA et al.; Retinoids, such as retinoic acid (RA), play a critical role in normal vertebrate development and physiology . However, embryonic exposure to excess retinoids also causes severe malformations . Retinoids bind RA receptors and retinoid X receptors, thus activating a plethora of genes . Separating the genes induced directly by retinoid-bound receptors from those induced subsequently by other transcription factors is difficult . The loose consensus defining known RA responsive elements (RAREs) further complicates this effort . We developed a yeast-based system to trap functional RAREs in the mouse genome . Several of the clones contain RAREs near RA-induced genes . Mammalian reporter gene analyses and EMSAs showed that these are bona fide RAREs . This functional genomics approach should identify RA-regulated genes that initiate critical signaling cascades in cells. Bioinformatics, 2003 Jan, 19(1), 30 - 6 Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps; Aires-de-Sousa J et al.; MOTIVATION: We propose representing individual positions in DNA sequences by virtual potentials generated by other bases of the same sequence . This is a compact representation of the neighbourhood of a base . The distribution of the virtual potentials over the whole sequence can be used as a representation of the entire sequence (SEQREP code) . It is a flexible code, with a length independent of the sequence size, does not require previous alignment, and is convenient for processing by neural networks or statistical techniques . RESULTS: To evaluate its biological significance, the SEQREP code was used for training Kohonen self-organizing maps (SOMs) in two applications: (a) detection of Alu sequences, and (b) classification of sequences encoding for HIV-1 envelope glycoprotein (env) into subtypes A-G . It was demonstrated that SOMs clustered sequences belonging to different classes into distinct regions . For independent test sets, very high rates of correct predictions were obtained (97% in the first application, 91% in the second) . Possible areas of application of SEQREP codes include functional genomics, phylogenetic analysis, detection of repetitions, database retrieval, and automatic alignment . AVAILABILITY: Software for representing sequences by SEQREP code, and for training Kohonen SOMs is made freely available from SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.dq.fct.unl.pt/qoa/jas/seqrep/bioinf2002 Nat Biotechnol, 2003 Jan, 21(1), 93 - 6 Epub 2002 Dec 23. Screening for gene function in chicken embryo using RNAi and electroporation; Pekarik V et al.; In the postgenomic era the elucidation of the physiological function of genes has become the rate-limiting step in the quest to understand the development and function of living organisms . Gene functions cannot be determined by high-throughput methods but require analysis in the context of the entire organism . This is particularly true in the developing vertebrate nervous system . Because of its easy accessibility in the egg, the chicken embryo has been the model of choice for developmental in vivo studies . However, its usefulness has been hampered by a lack of methods for genetic manipulation . Here we describe an approach that could compensate for this disadvantage . By combining gene silencing by dsRNA (through RNA interference, RNAi) with in ovo electroporation, we developed an efficient method to induce loss of gene function in vivo during the development of the chicken CNS . This method opens new possibilities for studying gene function not only by gain-of-function but also by loss-of-function approaches and therefore represents a new tool for functional genomics. Anat Rec A Discov Mol Cell Evol Biol, 2003 Jan, 270(1), 41 - 50 Acute oxygen sensing in cellular models: relevance to the physiology of pulmonary neuroepithelial and carotid bodies; Kemp PJ et al.; The combination of studies in native tissues and immortalised model systems during the last decade has made possible a deeper understanding of the physiology and functional morphology of arterial and airway oxygen sensors . Complementary and overlapping information from these earlier studies has allowed a detailed description of the cellular events that link decreased environmental oxygen to the release of physiologically important vasoactive transmitters . Since these basic pathways have now been defined functionally, what remains to be determined is the molecular identity of the specific proteins involved in the signal transduction pathways, and how these proteins interact to produce a full physiological response . With these goals clearly in sight, we have embarked upon a strategy that is a novel combination of proteomics and functional genomics . It is hoped this strategy will enable us to develop and refine the initial models in order to understand more completely the process of oxygen sensing in health and disease . Trends Genet, 2003 Jan, 19(1), 32 - 8 Hitchhiking mapping--functional genomics from the population genetics perspective; Schlotterer C; Several statistical tests based on population genetic theory are used to identify genes that have recently acquired a beneficial mutation . Here, I describe the extension of these tests to a multilocus approach for a genome-wide survey for genes that have been under recent positive selection . As this strategy could potentially identify genes with weak phenotypic effects, it will be very useful in population genetic approaches aimed at understanding adaptation processes in natural populations . Furthermore, this 'hitchhiking mapping' could also help in the functional characterization of genomes. BMC Bioinformatics . 2002 Dec 19;3(1):40. ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files; Bussow K et al.; BACKGROUND: Functional genomics involves the parallel experimentation with large sets of proteins . This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins . RESULTS: A Java program was developed for retrieval of protein and nucleic acid sequences and annotations from NCBI GenBank, using the XML sequence format . Annotations retrieved by ORFer include sequence name, organism and also the completeness of the sequence . The program has a graphical user interface, although it can be used in a non-interactive mode . For protein sequences, the program also extracts the open reading frame sequence, if available, and checks its correct translation . ORFer accepts user input in the form of single or lists of GenBank GI identifiers or accession numbers . It can be used to extract complete sets of open reading frames and protein sequences from any kind of GenBank sequence entry, including complete genomes or chromosomes . Sequences are either stored with their features in a relational database or can be exported as text files in Fasta or tabulator delimited format . The ORFer program is freely available at CONCLUSION: The ORFer program allows for fast retrieval of DNA sequences, protein sequences and their open reading frames and sequence annotations from GenBank . Furthermore, storage of sequences and features in a relational database is supported . Such a database can supplement a laboratory information system (LIMS) with appropriate sequence information. Nucleic Acids Res . 2002 Dec 15;30(24):e142. Novel retroviral vectors to facilitate expression screens in mammalian cells; Koh EY et al.; As tools for functional genomics, expression profiling and proteomics provide correlative data, while expression cloning screens can link genes directly to biological function . However, technical limitations of gene transfer, expression, and recovery of candidate genes have limited wider application of genome-wide expression screens . Here we describe the pEYK retroviral vectors, which maintain high titers and robust gene expression while addressing the major bottleneck of expression cloning--efficient candidate gene recovery . By exploiting schemes for enhanced PCR rescue or strategies for direct isolation of proviral DNA as plasmids in bacterial hosts, the pEYK vectors facilitate cDNA isolation from selected cells and enable rapid iteration of screens and genetic reversion analyses to validate gene candidates . These vectors have proven useful to identify genes linked to cell proliferation, senescence and apoptosis. J Neurobiol, 2003 Jan, 54(1), 272 - 82 Functional genomics of neural and behavioral plasticity; Hofmann HA; How does the environment, particularly the social environment, influence brain and behavior and what are the underlying physiologic, molecular, and genetic mechanisms? Adaptations of brain and behavior to changes in the social or physical environment are common in the animal world, either as short-term (i.e., modulatory) or as long-term modifications (e.g., via gene expression changes) in behavioral or physiologic properties . The study of the mechanisms and constraints underlying these dynamic changes requires model systems that offer plastic phenotypes as well as a sufficient level of quantifiable behavioral complexity while being accessible at the physiological and molecular level . In this article, I explore how the new field of functional genomics can contribute to an understanding of the complex relationship between genome and environment that results in highly plastic phenotypes . This approach will lead to the discovery of genes under environmental control and provide the basis for the study of the interrelationship between an individual's gene expression profile and its social phenotype in a given environmental context . Biomol Eng, 2003 Jan, 20(1), 7 - 20 Nucleotide replacement at two sites can be directed by modified single-stranded oligonucleotides in vitro and in vivo; Agarwal S et al.; Studies involving the alteration of DNA sequences by modified single-stranded oligonucleotides in vitro and in vivo have revealed potential applications for functional genomics . Repair of a replacement, deletion, or insertion mutation has already been achieved with molecules having lengths between 25 and 74 bases . But, other vector parameters still remain to be explored . Here, the position of the single base in the vector directing the alteration was examined and the optimal site was found to be at or near the center of the vector . If that position is staggered 3' or 5', the frequencies of gene repair in vitro decreases . The potential of a single vector to direct two nucleotide changes at a specific site in a target sequence was also examined . Both targeted bases are corrected together at the same frequency if the sites are separated by three bases, but conversion linkage decreases precipitously when the distance is expanded to 15 and 27 nucleotides, respectively . These results suggest that single oligonucleotides can be used to direct nucleotide exchange at two independent sites, a reaction characteristic that may be useful for many genomics applications. Trends Biotechnol, 2003 Jan, 21(1), 9 - 13 Promoters can contribute to the elucidation of protein function; Werner T; Protein interaction maps are valuable tools in the understanding of the actions of genes and proteins in a real-life context . However, many proteins and genes interact functionally - without physical contact - via transcriptional coregulation of the genes, which is partially manifested in functional promoter structures called promoter modules . Here, the example of interleukin 9 (IL-9) induction by IL-1 and tumour necrosis factor (TNF) is used to demonstrate how comparative promoter analysis can identify a shared promoter module and thus indicate the crucial partners . This strategy can be used for genes from a small initial set of coregulated genes, such as can be derived from expression array data . The combination of expression and promoter analysis with proteomics should be considered as an important link in functional genomics. Trends Plant Sci, 2002 Dec, 7(12), 535 - 8 Moss transcriptome and beyond; Rensing SA et al.; The ancient land plant Physcomitrella patens is a model system that is becoming increasingly important for plant functional genomics because gene knockouts can be produced with relative ease . Recently, several EST-sequencing projects have been launched as a first step towards a thorough functional characterization of the moss . However, for careful comparison with other plant model systems, the complete genomic sequence is needed as well as the transcriptome. Trends Plant Sci, 2002 Dec, 7(12), 531 - 4 Transcription factors do it together: the hows and whys of studying protein-protein interactions; Immink RG et al.; Protein-protein interactions are intrinsic to virtually every cellular process . Recent breakthroughs in techniques to study protein-interaction and the availability of fully sequenced plant genomes have attracted many plant scientists to undertake the first steps in the field of protein interactions . High-throughput screening systems allow the discovery of protein functions . Even without performing laborious functional assays, in planta functional homologues and redundant proteins can be accurately predicted based on protein-interaction maps . Therefore, protein-protein-interaction screenings are an essential supplement to the current functional-genomics toolbox. J Chem Ecol, 2002 Oct, 28(10), 1919 - 34 Marine tannins: the importance of a mechanistic framework for predicting ecological roles; Arnold TM et al.; Since chemical ecology emerged as a field of marine science, it has been strongly influenced by studies of chemically mediated interactions in land-based systems . Marine chemical ecologists, like their terrestrial counterparts, initially focused on identifying natural products and evaluating the potential ecological roles of these products as defenses, attractants, or other cues . Now, like our land-based colleagues, we must increase our focus on the physiological and biochemical mechanisms that underlie the chemical interactions, paying particular attention to regulation of biosynthetic pathways, within-plant and between-plant signaling cues, and comparative and functional genomics . Here, we review the current state of knowledge regarding a heterogenous group of macrophyte natural products, the marine tannins and simple phenolics, to illustrate how such information is critical to future attempts to predict their ecological roles. Annu Rev Physiol, 2003, 65, 203 - 30 Epub 2002 May 01. Functional genomics and the comparative physiology of hypoxia; Powell FL; Comparative physiology has proven a powerful approach to our understanding of how animals function under hypoxic conditions and to identifying potential adaptations to environmental oxygen levels . This review considers the potential for using a similar comparative approach with functional genomics to understand the genetic basis of such physiological processes and evolutionary adaptations . Comparative functional genomics is currently limited by genome data, which are available for only a few model organisms . However, comparative studies between model organisms of the same species having slightly different genomes (e.g., in-bred strains of laboratory rodents, transgenic mice, and consomic rats) demonstrate the types of results, as well as the analytical challenges, that are possible if comparative functional genomics is applied to more species . Results from wild and domestic animal studies suggest new models to investigate physiological and evolutionary responses to oxygen levels with functional genomics. Comp Biochem Physiol B Biochem Mol Biol, 2002 Dec, 133(4), 559 - 70 Functional genomics and sexual differentiation in amphibians; Bogi C et al.; In Xenopus laevis the basic mechanisms underlying sexual differentiation were investigated by determining time courses of sexual steroids and their corresponding receptors during complete larval development from egg to juveniles . Androgens as well as estradiol (E2) are derived from maternal origin and accumulate in hatching tadpoles . Sexual steroid contents decreased rapidly after hatching and rose again at the end of metamorphosis indicating endogenous production . In parallel the mRNA expression for corresponding androgen (AR) and estrogen receptors (ER) was measured by means of semiquantitative RT-PCR . Both receptor mRNAs increased dramatically just after hatching and decreased only moderately until end of metamorphosis . In female juveniles E2 and ER-mRNA levels were higher compared with males . Treatment by exogenous E2 elevated both, ER- and AR-mRNA, indicating stimulatory functions of E2 for gene expression of both receptors . Effects on sexual differentiation during larval development were achieved by treatment with E2 and the antiandrogen cyproterone acetate both causing feminization, the antiestrogen tamoxifen resulting in neutralization, and the androgens, methyltestosterone and dihydrotestosterone, but not testosterone, leading to masculinization . The data presented are in accordance with further recent findings and suggest a new hypothesis for functional genomics in sexual differentiation of amphibians. Curr Opin Chem Biol, 2002 Dec, 6(6), 765 - 72 Modular design of artificial transcription factors; Ansari AZ et al.; Eukaryotic transcription factors are composed of interchangeable modules . This has led to the design of a wide variety of modular artificial transcription factors (ATFs) that can stimulate or inhibit the expression of targeted genes . The ability to regulate the expression of any targeted gene using a 'programmable' ATF offers a powerful tool for functional genomics and bears tremendous promise in developing the field of transcription-based therapeutics. Comb Chem High Throughput Screen, 2002 Sep, 5(6), 429 - 40 High-density synthetic peptide microarrays: emerging tools for functional genomics and proteomics; Frank R; New approaches for manufacturing and application of peptide arrays on planar surfaces are emerging, thereby opening advanced opportunities to probe the expression and function of the proteome . In complementing DNA and protein array analyses, peptide fragment screening directly addresses functional protein interaction sites, leading to a detailed insight into the discovered molecular recognition events, placing them in the context of the whole genome, and even allowing rapid determination of the chemical nature of these interactions . This information can then be transferred into powerful small peptide tools that interfere with these interactions in vivo and help to link targets with phenotypes . With the spreading of new peptide array tools, peptide screening will extend its impact on modern genome-driven molecular biology . This will advance the systematic discovery and validation of new pharmaceutical targets as well as the development of potent molecular diagnostics for medical and ecological monitoring. Comb Chem High Throughput Screen, 2002 Nov, 5(7), 511 - 22 In Ssarch of new anti-bacterial target genes: a comparative/structural genomics approach; Claverie JM et al.; We outline a joint academic/industrial (CNRS/AVENTIS) functional genomics project aiming at the discovery of new anti-bacterial gene targets . Starting from all publicly available bacterial genomes, a subset of the most evolutionary conserved protein-coding genes has been identified . We retained genes with clear homolog in E . coli and at least one gram-positive bacterium among B.subtilis, M . tuberculosis, L . lactis or S . pyogenes . This subset was further reduced to genes encoding non-membrane proteins of unknown or hypothetical functions . The 221 E . coli Open Reading Frames (ORFs) identified through this comprehensive bioinformatic analysis are now submitted to a systematic 3-D structure determination protocol including cloning, protein expression and purification, crystallisation and X-ray diffraction . Our strategy was designed to focus on promising wide-spectrum targets as well as original biochemical pathways . Bioinformatics is used throughout all phases of project, including the initial large-scale comparative genomics analyses, the purification/expression and crystallisation stages for the detection of helpful sequence-specific features (e.g . cofactor binding motifs, non-structured N- or C- term extremities, etc ), and finally for the interpretation of the structures in conjunction with multiple sequence alignments for the identification of key residues, interaction areas on molecular surfaces, and overall function predictions. Plant Cell, 2002 Dec, 14(12), 2985 - 94 A high-throughput Arabidopsis reverse genetics system; Sessions A et al.; A collection of Arabidopsis lines with T-DNA insertions in known sites was generated to increase the efficiency of functional genomics . A high-throughput modified thermal asymmetric interlaced (TAIL)-PCR protocol was developed and used to amplify DNA fragments flanking the T-DNA left borders from approximately 100000 transformed lines . A total of 85108 TAIL-PCR products from 52964 T-DNA lines were sequenced and compared with the Arabidopsis genome to determine the positions of T-DNAs in each line . Predicted T-DNA insertion sites, when mapped, showed a bias against predicted coding sequences . Predicted insertion mutations in genes of interest can be identified using Arabidopsis Gene Index name searches or by BLAST (Basic Local Alignment Search Tool) search . Insertions can be confirmed by simple PCR assays on individual lines . Predicted insertions were confirmed in 257 of 340 lines tested (76%) . This resource has been named SAIL (Syngenta Arabidopsis Insertion Library) and is available to the scientific community at www.tmri.org. Nature, 2002 Dec 5, 420(6915), 582 - 6 Human chromosome 21 gene expression atlas in the mouse; Reymond A et al.; Genome-wide expression analyses have a crucial role in functional genomics . High resolution methods, such as RNA in situ hybridization provide an accurate description of the spatiotemporal distribution of transcripts as well as a three-dimensional 'in vivo' gene expression overview . We set out to analyse systematically the expression patterns of genes from an entire chromosome . We chose human chromosome 21 because of the medical relevance of trisomy 21 (Down's syndrome) . Here we show the expression analysis of all identifiable murine orthologues of human chromosome 21 genes (161 out of 178 confirmed human genes) by RNA in situ hybridization on whole mounts and tissue sections, and by polymerase chain reaction with reverse transcription on adult tissues . We observed patterned expression in several tissues including those affected in trisomy 21 phenotypes (that is, central nervous system, heart, gastrointestinal tract, and limbs) . Furthermore, statistical analysis suggests the presence of some regions of the chromosome with genes showing either lack of expression or, to a lesser extent, co-expression in specific tissues . This high resolution expression 'atlas' of an entire human chromosome is an important step towards the understanding of gene function and of the pathogenetic mechanisms in Down's syndrome. Nature, 2002 Dec 5, 420(6915), 563 - 73 Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs; Okazaki Y et al.; Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts . There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones . Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences . These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database . Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome . 41% of all transcriptional units showed evidence of alternative splicing . In protein-coding transcripts, 79% of splice variations altered the protein product . Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs . The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics. Int J Parasitol, 2002 Dec 19, 32(14), 1727 - 37 Functional genomics of gam56: characterisation of the role of a 56 kilodalton sexual stage antigen in oocyst wall formation in Eimeria maxima; Belli SI et al.; Gam56 (M(r) 56,000) is an antigen found in the sexual (macrogametocyte) stage of the intestinal parasite Eimeria maxima that is implicated in protective immunity . The gene (gam56) encoding this protein was cloned and sequenced . It is a single-copy, intronless gene, that localises to a 1,754 bp transcript, and is first detected at 120 h p.i . The gene predicts two distinct protein domains; a tyrosine-serine rich region, composed of amino acids implicated in oocyst wall formation in Eimeria spp., and a proline-methionine rich region often detected in extensins, protein components of plant cell walls . The tyrosine-serine rich region predicts a secondary structure commonly seen in the structural protein fibroin, a component of the cocoon of the caterpillar Bombyx mori . The inference that gam56 is a structural component of the oocyst wall was confirmed when a specific antibody to gam56 recognised the wall forming bodies in macrogametocytes, and the walls of oocysts and sporocysts . Together, these data identify a developmentally regulated, sexual stage gene in E . maxima that shares primary and secondary structure features in common with intrinsic structural proteins in other parasites such as Schistosoma mansoni and Fasciola hepatica, and other organisms across different phyla, including the caterpillar Bombyx mori . In addition, these findings provide evidence for the molecular mechanisms underlying oocyst wall formation in Eimeria and the role of gametocyte antigens in this process. Proc AMIA Symp . 2002;:86-90. Representation of roles in biomedical ontologies: a case study in functional genomics; Burgun A et al.; OBJECTIVE: Representing roles, i.e . functions of proteins, sequences and structures, is the cornerstone of knowledge representation in functional genomics . The objective of this study is to investigate representation of roles as functional categories or associative relations . We focus on GeneOntology (GO) and the UMLS and take examples from iron metabolism . METHODS: The terms corresponding to the main proteins involved in iron metabolism were mapped to GO (including the annotations) and the UMLS . The representation of their biological roles was then analyzed . RESULTS: Functional aspects are represented in both GO and the UMLS . However, the granularity may not be appropriate . DISCUSSION: Advantages and limits of functional categories and associative relations are discussed. Nat Rev Drug Discov, 2002 Dec, 1(12), 951 - 60 The use and analysis of microarray data; Butte A; Functional genomics is the study of gene function through the parallel expression measurements of genomes, most commonly using the technologies of microarrays and serial analysis of gene expression . Microarray usage in drug discovery is expanding, and its applications include basic research and target discovery, biomarker determination, pharmacology, toxicogenomics, target selectivity, development of prognostic tests and disease-subclass determination . This article reviews the different ways to analyse large sets of microarray data, including the questions that can be asked and the challenges in interpreting the measurements. Curr Opin Biotechnol, 2002 Oct, 13(5), 508 - 11 Phytochemicals in plants: genomics-assisted plant improvement for nutritional and health benefits; Grusak MA; Plants are an important source of essential nutrients and health-beneficial components that are crucial for human life . Because the intake of these phytochemicals is not always adequate, the resources of plant biotechnology are being used to enhance the nutritional quality of our plant-based food supply . Various improvement strategies are feasible, depending on whether the phytochemical target is a major or minor constituent . Recent efforts in gene discovery and functional genomics are providing the necessary understanding to develop and evaluate different approaches to manipulate phytochemical composition. Curr Opin Biotechnol, 2002 Oct, 13(5), 453 - 8 Antiprogestin-controllable transgene regulation in vivo; Nordstrom JL; Gene control systems that provide temporal and spatial regulation of transgene expression in response to orally delivered drugs are needed for advances in functional genomics, models of human disease and gene therapy . A regulation system based on the altered binding and activation properties of a truncated ligand-binding domain derived from the progesterone receptor has been shown to be effective in providing tissue-specific, antiprogestin-controllable gene expression in transgenic mice, transgenic fruit flies and animals that have been administered viral-based or plasmid-based gene therapy vectors. Dev Dyn, 2002 Dec, 225(4), 422 - 33 Xenopus, the next generation: X . tropicalis genetics and genomics; Hirsch N et al.; A small, fast-breeding, diploid relative of the frog Xenopus laevis, Xenopus tropicalis, has recently been adopted for research in developmental genetics and functional genomics . X . tropicalis shares advantages of X . laevis as a classic embryologic system, but its simpler genome and shorter generation time make it more convenient for multigenerational genetic, genomic, and transgenic approaches . Its embryos closely resemble those of X . laevis, except for their smaller size, and assays and molecular probes developed in X . laevis can be readily adapted for use in X . tropicalis . Genomic manipulation techniques such as gynogenesis facilitate genetic screens, because they permit the identification of recessive phenotypes after only one generation . Stable transgenic lines can be used both as in vivo reporters to streamline a variety of embryologic and molecular assays, or to experimentally manipulate gene expression through the use of binary constructs such as the GAL4/UAS system . Several mutations have been identified in wild-caught animals and during the course of generating inbred lines . A variety of strategies are discussed for conducting and managing genetic screens, obtaining mutations in specific sequences, achieving homologous recombination, and in developing and taking advantage of the genomic resources for Xenopus tropicalis . Nat Genet, 2002 Dec, 32 Suppl, 541 - 6 Functional exploration of the C . elegans genome using DNA microarrays; Reinke V; Global changes in gene expression underlie developmental processes such as organogenesis, embryogenesis and aging in Caenorhabditis elegans . Recently developed methods allow gene expression profiles to be determined selectively for individual tissues and cell types . Results from both whole-animal and tissue-specific expression profiling have provided an unprecedented view into genome organization and gene function . Integration of these results with other types of functional genomics data gathered from RNA-mediated interference and yeast two-hybrid analyses will allow rapid identification and exploration of the complex functional gene networks that govern C . elegans development. Ann Med, 2002, 34(5), 357 - 79 Pharmacogenomics for the treatment of dementia; Cacabelos R; Alzheimer's disease (AD) is a genetically complex disorder associated with multiple genetic defects either mutational or of susceptibility . Current AD genetics does not explain in full the etiopathogenesis of AD, suggesting that environmental factors and/or epigenetic phenomena may also contribute to AD pathology and phenotypic expression of dementia . The genomics of AD is still in its infancy, but is helping us to understand novel aspects of the disease including genetic epidemiology, multifactorial risk factors, pathogenic mechanisms associated with genetic networks and genetically-regulated metabolic cascades . AD genomics is also fostering new strategies in pharmacogenomic research and prevention . Functional genomics, proteomics, pharmacogenomics, high-throughput methods, combinatorial chemistry and modern bioinformatics will greatly contribute to accelerating drug development for AD and other complex disorders . The multifactorial genetic dysfunction in AD includes mutational loci (APP, PS1, PS2) and diverse susceptibility loci (APOE, A2M, AACT, LRP1, IL1A, TNF, ACE, BACE, BCHE, CST3, MTHFR, GSK3B, NOS3) distributed across the human genome, probably converging in common pathogenic mechanisms that lead to premature neuronal death . Genomic associations integrate polygenic matrix models to elucidate the genomic organization of AD in comparison to the control population . Using APOE-related monogenic models it has been demonstrated that the therapeutic response to drugs (e.g., cholinesterase inhibitors, non-cholinergic compounds) in AD is genotype-specific . A multifactorial therapy combining three different drugs yielded positive results during 6-12 months in approximately 60% of the patients . With this therapeutic strategy, APOE-4/4 carriers were the worst responders and patients with the APOE-3/4 genotype were the best responders . Other polymorphic variants (PS1, PS2) also influence the therapeutic response to different drugs in AD patients, suggesting that the final pharmacological outcome is the result of multiple genomic interactions, including AD-related genes and genes associated with drug metabolism, disposition, and elimination . The pharmacogenomics of AD may contribute in the future to optimise drug development and therapeutics, increasing efficacy and safety, and reducing side-effects and unnecessary costs. Hepatology, 2002 Dec, 36(6), 1313 - 25 Gene array analysis and the liver; Shackel NA et al.; Functional genomics methods promise a previously unparalleled high-throughput examination of intrahepatic gene expression . Profiling transcriptomes as well as examining the coordinate expression of many genes in diverse pathobiologic pathways is now possible with techniques such as gene array analysis . However, the nature of the hepatic transcriptome, limitations of the functional genomics methodologies used, and analysis of the data generated are often poorly understood . Further, the use of replicates during analysis and the downstream confirmation of results using a supplemental methodology are important but frequently neglected aspects of experimental design . This review presents an overview of functional genomics methodologies in the organ-specific context of studying intrahepatic gene expression . The focus of the review is the most widely used functional genomic methodology, gene array analysis . The nature of the hepatic transcriptome is discussed, together with a summary of gene array analysis methodologies . Analysis of data generated by gene array analysis, determination of intrahepatic cellular origin of transcript expression, and studies of intrahepatic gene expression using gene array analysis are also reviewed . Finally, the importance of a coordinate experimental approach examining both liver protein and mRNA expression is presented. Eur J Biochem, 2002 Dec, 269(23), 5753 - 8 Optimizing the delivery systems of chimeric RNA.DNA oligonucleotides; Liang L et al.; Special oligonucleotides for targeted gene correction have attracted increasing attention recently, one of which is the chimeric RNA.DNA oligonucleotide (RDO) system . RDOs for targeted gene correction were first designed in 1996, and are typically 68 nucleotides in length including continuous RNA and DNA sequences (RNA is 2'-O-methyl-modified) . They have a 25 bp double stranded region homologous to the targeted gene, two hairpin ends of T loop and a 5 bp GC clamp, that give the molecule much greater stability {Fig . 1} . One mismatch site in the middle of the double-stranded region is designed for targeted gene therapy . RDOs have been used recently for targeted gene correction of point mutations both in vitro and in vivo, but many problems must be solved before clinical application . One of the solutions is to optimize the delivery vectors for RDOs . To date, few RDO delivery systems have been used . Therefore, new vectors should be tried for RDO transfer, such as the use of nanoparticles . Additionally, different kinds of modifications should be applied to RDO carrier systems to increase the total correction efficiency in vivo . Only with the development of delivery systems can RDOs be used for gene therapy, and successfully applied to functional genomics. Circ Res, 2002 Nov 15, 91(10), 866 - 76 Derivation and potential applications of human embryonic stem cells; Gepstein L; Embryonic stem cells are pluripotent cell lines that are derived from the blastocyst-stage early mammalian embryo . These unique cells are characterized by their capacity for prolonged undifferentiated proliferation in culture while maintaining the potential to differentiate into derivatives of all three germ layers . During in vitro differentiation, embryonic stem cells can develop into specialized somatic cells, including cardiomyocytes, and have been shown to recapitulate many processes of early embryonic development . The present review describes the derivation and unique properties of the recently described human embryonic stem cells as well as the properties of cardiomyocytes derived using this unique differentiating system . The possible applications of this system in several cardiac research areas, including developmental biology, functional genomics, pharmacological testing, cell therapy, and tissue engineering, are discussed . Because of their combined ability to proliferate indefinitely and to differentiate to mature tissue types, human embryonic stem cells can potentially provide an unlimited supply of cardiomyocytes for cell therapy procedures aiming to regenerate functional myocardium . However, many obstacles must still be overcome on the way to successful clinical utilization of these cells. Curr Issues Mol Biol, 2002 Oct, 4(4), 129 - 46 "A system biology" approach to bioinformatics and functional genomics in complex human diseases: arthritis; Attur MG et al.; Human and other annotated genome sequences have facilitated generation of vast amounts of correlative data, from human/animal genetics, normal and disease-affected tissues from complex diseases such as arthritis using gene/protein chips and SNP analysis . These data sets include genes/proteins whose functions are partially known at the cellular level or may be completely unknown (e.g . ESTs) . Thus, genomic research has transformed molecular biology from "data poor" to "data rich" science, allowing further division into subpopulations of subcellular fractions, which are often given an "-omic" suffix . These disciplines have to converge at a systemic level to examine the structure and dynamics of cellular and organismal function . The challenge of characterizing ESTs linked to complex diseases is like interpreting sharp images on a blurred background and therefore requires a multidimensional screen for functional genomics ("functionomics") in tissues, mice and zebra fish model, which intertwines various approaches and readouts to study development and homeostasis of a system . In summary, the post-genomic era of functionomics will facilitate to narrow the bridge between correlative data and causative data by quaint hypothesis-driven research using a system approach integrating "intercoms" of interacting and interdependent disciplines forming a unified whole as described in this review for Arthritis. Curr Issues Mol Biol, 2002 Oct, 4(4), 101 - 10 Role of genetic and expression profiling in pharmacogenomics: the changing face of patient management; Pagliarulo V et al.; As the determination of gene sequences and their function gains speed at the dawn of the third millennium, biomedical research efforts are oriented towards definition of the genetic and molecular expression patterns that may drive different disease . A major part of these efforts is addressed to the definition of inter-individual variations that are expected to become integral for treatment planning, in terms of efficacy and adverse effects of drugs . It is this thrust on genome-based 'rational therapeutics' that is hoped to progressively lead to the era of 'personalized medicine' . This approach uses the technological expertise from genomics and functional genomics to define, predict and monitor the nature of the response of an individual to drugs, and to rationally design newer drugs . In the present review we will conduct our readers through an understanding of the fundamentals of pharmacogenomics and of the technologies currently available that are advancing this relatively new science . Conversely, there are issues raised that concern how medical practice is preparing itself to implement new alternatives for therapeutical interventions and finally, how to respect patient confidentiality and rights. Int J Cancer, 2002 Dec 10, 102(5), 487 - 91 Replication efficiency and sequence analysis of full-length hepatitis B virus isolates from hepatocellular carcinoma tissues; Lin X et al.; Prolonged replication of hepatitis B virus (HBV) in liver tissues of hepatitis B patients has been considered as an important risk factor for the development of malignancy . Few studies on full-length HBV sequencing in association with the replication efficiency of isolates from HCC tissues have been reported . To study the structural and functional genomics of HBV isolates from Chinese hepatocellular carcinoma (HCC) patients, full-length HBV genomes were amplified from 6 HBV-marker positive HCC tissues and used to transfect HepG2 cells . Five of 6 isolates showed high replicative efficiency . All isolates were of genotype C and "hot-spots" mutations were detected in the B cell and T helper (Th) cell epitopes of the envelope and the core region . In addition, the X region of 2 isolates contained a stop-codon mutation that was predicted to result in a truncated X protein . High replicative HBV immune escape mutants that persist in infected hepatocytes could be 1 of the important factors to initiate pathological processes for the development of HCC in Chinese patients . Nature, 2002 Nov 14, 420(6912), 224 - 30 Engineered gene circuits; Hasty J et al.; A central focus of postgenomic research will be to understand how cellular phenomena arise from the connectivity of genes and proteins . This connectivity generates molecular network diagrams that resemble complex electrical circuits, and a systematic understanding will require the development of a mathematical framework for describing the circuitry . From an engineering perspective, the natural path towards such a framework is the construction and analysis of the underlying submodules that constitute the network . Recent experimental advances in both sequencing and genetic engineering have made this approach feasible through the design and implementation of synthetic gene networks amenable to mathematical modelling and quantitative analysis . These developments have signalled the emergence of a gene circuit discipline, which provides a framework for predicting and evaluating the dynamics of cellular processes . Synthetic gene networks will also lead to new logical forms of cellular control, which could have important applications in functional genomics, nanotechnology, and gene and cell therapy. Planta, 2002 Nov, 216(1), 107 - 19 Epub 2002 Nov 12. Family business: the multidrug-resistance related protein (MRP) ABC transporter genes in Arabidopsis thaliana; Kolukisaoglu HU et al.; Despite the completion of the sequencing of the entire genome of Arabidopsis thaliana (L.) Heynh., the exact determination of each single gene and its function remains an open question . This is especially true for multigene families . An approach that combines analysis of genomic structure, expression data and functional genomics to ascertain the role of the members of the multidrug-resistance-related protein ( MRP) gene family, a subfamily of the ATP-binding cassette (ABC) transporters from Arabidopsis is presented . We used cDNA sequencing and alignment-based re-annotation of genomic sequences to define the exact genic structure of all known AtMRP genes . Analysis of promoter regions suggested different induction conditions even for closely related genes . Expression analysis for the entire gene family confirmed these assumptions . Phylogenetic analysis and determination of segmental duplication in the regions of AtMRP genes revealed that the evolution of the extraordinarily high number of ABC transporter genes in plants cannot solely be explained by polyploidisation during the evolution of the Arabidopsis genome . Interestingly MRP genes from Oryza sativa L . (rice; OsMRP) show very similar genomic structures to those from Arabidopsis . Screening of large populations of T-DNA-mutagenised lines of A . thaliana resulted in the isolation of AtMRP insertion mutants . This work opens the way for the defined analysis of a multigene family of important membrane transporters whose broad variety of functions expands their traditional role as cellular detoxifiers. Plant Physiol, 2002 Nov, 130(3), 1109 - 20 Global changes in gene expression in response to high light in Arabidopsis; Rossel JB et al.; A range of environmental conditions can lead to oxidative stress; thus, a prompt and effective response to oxidative stress is crucial for the survival of plants . Microarray and northern-blot analyses were performed toward the identification of the factors and signaling pathways that enable plants to limit oxidative damage caused by exposure to high light (HL) . Arabidopsis plants grown under moderate light (100 micromol m(-2) s(-1)) were exposed to HL (1,000 micromol m(-2) s(-1)) for 1 h . The microarray analyses revealed that exposure of Arabidopsis to HL caused an increase in known antioxidant genes, as well as several unknown genes . Some of these unknown genes had homologies to possible regulatory genes and metabolic enzymes . Furthermore, it was found that a range of chaperones were up-regulated in the HL treatment and that this induction was specifically due to the HL stress . The temporal expression under HL and different oxidative stress conditions of a subset of HL-responsive genes was confirmed via northern-blot analysis . Results from the arrays were also compared with publicly available microarray data sets from a range of different stress conditions at the Arabidopsis Functional Genomics Consortium . This cross comparison enabled the identification of genes that may be induced by changes in redox poise . Finally, to determine if the genes that were differentially expressed by HL stress were under similar transcriptional control, we analyzed the promoter sequences for the presence of common motifs. Lancet Oncol, 2002 Nov, 3(11), 672 - 83 Antisense therapy for cancer--the time of truth; Jansen B et al.; The recent acceleration in the identification and characterisation of new molecular targets for cancer and the limited effectiveness of conventional treatment strategies has focused considerable interest on the development of new types of anticancer agents . These new drugs are hoped to be highly specific for malignant cells with a favorable side-effect profile due to well-defined mechanisms of action . Antisense oligonucleotides are one such class of new agent--they are short, synthetic stretches of DNA which hybridise with specific mRNA strands that correspond to target genes . By binding to the mRNA, the antisense oligonucleotides prevent the sequence of the target gene being converted into a protein, thereby blocking the action of the gene . Several genes known to be important in the regulation of apoptosis, cell growth, metastasis, and angiogenesis, have been validated as molecular targets for antisense therapy . Furthermore, new targets are rapidly being uncovered through coordinated functional genomics and proteomics initiatives . Phosphorothioate oligonucleotides are the current gold standard for antisense therapy; they have acceptable physical and chemical properties and show reasonable resistance to nucleases . Recently, new generations of these phosphorothioate oligonucleotides that contain 2'-modified nucleoside building blocks to enhance RNA binding affinity and decrease indirect toxic effects have been developed . Antisense therapeutics are, after decades of difficulties, finally close to fulfilling their promise in the clinic. Acta Biochim Pol, 2002, 49(3), 553 - 69 Mice and humans: chromosome engineering and its application to functional genomics; Klysik J; Functional modeling of human genes and diseases requires suitable mammalian model organisms . For its genetic malleability, the mouse is likely to continue to play a major role in defining basic genetic traits and complex pathological disorders . Recently, gene targeting techniques have been extended towards developing new engineering strategies for generating extensive lesions and rearrangements in mouse chromosomes . While these advances create new opportunities to address similar aberrations observed in human diseases, they also open new ways of scaling-up mutagenesis projects that try to catalogue and annotate cellular functions of mammalian genes. Parasitol Int, 2002 Dec, 51(4), 319 - 25 Functional genomics of parasitic worms: the dawn of a new era; Brooks DR et al.; The study of gene function in parasitic worms is technically demanding due to difficulties associated with life-cycle propagation and, hence, molecular genetics . Exploitation of the free-living nematode, Caenorhabditis elegans, coupled with recent major advances in molecular studies of parasitic nematodes, have opened up new avenues for understanding the biology of these parasites and present opportunities for novel strategies of therapeutic intervention and control. Arch Microbiol, 2002 Dec, 178(6), 395 - 403 Epub 2002 Sep 18. Cellular differentiation in the cyanobacterium Nostoc punctiforme; Meeks JC et al.; Nostoc punctiforme is a phenotypically complex, filamentous, nitrogen-fixing cyanobacterium, whose vegetative cells can mature in four developmental directions . The particular developmental direction is determined by environmental signals . The vegetative cell cycle is maintained when nutrients are sufficient . Limitation for combined nitrogen induces the terminal differentiation of heterocysts, cells specialized for nitrogen fixation in an oxic environment . A number of unique regulatory events and genes have been identified and integrated into a working model of heterocyst differentiation . Phosphate limitation induces the transient differentiation of akinetes, spore-like cells resistant to cold and desiccation . A variety of environmental changes, both positive and negative for growth, induce the transient differentiation of hormogonia, motile filaments that function in dispersal . Initiation of the differentiation of heterocysts, akinetes and hormogonia are hypothesized to depart from the vegetative cell cycle, following separate and distinct events . N . punctiforme also forms nitrogen-fixing symbiotic associations; its plant partners influence the differentiation and behavior of hormogonia and heterocysts . N . punctiforme is genetically tractable and its genome sequence is nearly complete . Thus, the regulatory circuits of three cellular differentiation events and symbiotic interactions of N . punctiforme can be experimentally analyzed by functional genomics. Nat Rev Immunol, 2002 Nov, 2(11), 881 - 9 Opinion: Interpretation of the complexity of innate immune responses by functional genomics; Ricciardi-Castagnoli P et al.; Understanding how the immune system is regulated and responds to pathogens will require whole-system approaches, because the study of single immunological parameters has, so far, been unable to unlock immune-system complexity . Global transcription analysis using microarray technologies provides a new approach to the description of complex biological phenomena . Here, we discuss insights into innate immunity that have been provided by genome-wide approaches and their impact on the interpretation of immune-system complexity. Bull Acad Natl Med, 2002, 186(5), 895 - 905; discussion 905-6 {From genomics to post-genomics: back to the origins?}; Jeanteur P; The purpose of this review is to emphasize the multiplicity and importance, physiological and pathological, of gene regulation levels which operate after the initiation step of transcription . Albeit crucial, this step is only the first one of a long cascade of events which eventually end up in the selection of functional messengers appropriate to the nature of the cells and to their immediate needs . Throughout this long pathway, of which only a few steps will be mentioned here, this review will attempt to address the central role played by RNA, not only as a substrate but as an actor of its own regulation . Emphasis will be put on the numerous connections with pathology up to the development of new therapeutics specifically targeting RNA . It highlights the perennity of basic questions, nearly half a century old, for which genomics, short of new concepts, will provide the databases and tools required to access to the immense field of functional genomics, the only one likely to bring relevant answers for therapeutics. Proc Natl Acad Sci U S A, 2002 Nov 12, 99(23), 14710 - 5 Epub 2002 Oct 31. A single point mutation in ecdysone receptor leads to increased ligand specificity: implications for gene switch applications; Kumar MB et al.; The ecdysone receptor (EcR), a member of the nuclear receptor superfamily, plays an important role in regulating development and reproduction in insects . The EcR binds to ecdysteroids and regulates transcription of genes that contain ecdysone response elements . The EcR has been used to develop inducible gene switches for efficient regulation of foreign genes in applications such as gene therapy, protein production, and functional genomics . An EcR {Choristoneura fumiferana EcR (CfEcR)} homology model was constructed, and 17 amino acid residues were identified as critical for 20-hydroxyecdysone binding . Mutation of these amino acids followed by analysis of these mutants in transactivation (in insect and mammalian cells and in vivo in mice) and ligand-binding assays identified one particular mutant (A110P) that failed to respond to steroids, but its response to the diacylhydrazine nonsteroidal ligands RG-102240 (GS(TM)E) and RG-102317 was unaffected . This steroid-insensitive EcR mutant has potential gene switch applications in insects and plants that have endogenous ecdysteroids . In addition, this mutant would be also useful for developing orthogonal EcR-ligand pairs for simultaneous regulation of multiple genes in the same cell. Biochem Biophys Res Commun, 2002 Nov 8, 298(4), 566 - 73 Functional improvement of antibody fragments using a novel phage coat protein III fusion system; Jensen KB et al.; Functional expressions of proteins often depend on the presence of host specific factors . Frequently recombinant expression strategies of proteins in foreign hosts, such as bacteria, have been associated with poor yields or significant loss of functionality . Improvements in the performance of heterologous expression systems will benefit present-day quests in structural and functional genomics where high amounts of active protein are required . One example, which has been the subject of considerable interest, is recombinant antibodies or fragments thereof as expressions of these in bacteria constitute an easy and inexpensive method compared to hybridoma cultures . Such approaches have, however, often suffered from low yields and poor functionality . A general method is described here which enables expressions of functional antibody fragments when fused to the amino-terminal domain(s) of the filamentous phage coat protein III . Furthermore, it will be shown that the observed effect is neither due to improved stability nor increased avidity. Nat Rev Drug Discov, 2002 Aug, 1(8), 599 - 608 The use of constitutively active GPCRs in drug discovery and functional genomics; Chalmers DT et al.; The complete sequencing of the human genome has afforded researchers the opportunity to identify novel G-protein-coupled receptors (GPCRs) that are expressed in human tissues . The successful identification of hundreds of GPCRs represents the single greatest opportunity for novel drug development today . However, the lack of identified ligands for these GPCRs has limited their utility for traditional drug discovery approaches that focus on ligand-based assay methods to discover and pharmacologically characterize drug candidates . Here, we review the use of constitutively activated GPCRs in the discovery pathway, both as a means to overcome the limitations of traditional drug discovery at novel GPCRs and as a tool to investigate the functionality of these receptors. Blood, 2002 Dec 15, 100(13), 4655 - 9 Epub 2002 Aug 22. The zebrafish mutant gene chardonnay (cdy) encodes divalent metal transporter 1 (DMT1); Donovan A et al.; Iron is an essential nutrient required for the function of all cells, most notably for the production of hemoglobin in red blood cells . Defects in the mechanisms of iron absorption, storage, or utilization can lead to disorders of iron-limited erythropoiesis or iron overload . In an effort to further understand these processes, we have used the zebrafish as a genetic system to study vertebrate iron metabolism . Here we characterized the phenotype of chardonnay (cdy), a zebrafish mutant with hypochromic, microcytic anemia, and positioned the mutant gene on linkage group 11 . The cdy gene was isolated by a functional genomics approach in which we used a combination of expression studies, sequence analyses, and radiation hybrid panel mapping . We identified erythroid-specific genes using a whole embryo mRNA in situ hybridization screen and placed these genes on the zebrafish genomic map . One of these genes encoded the iron transporter divalent metal transporter 1 (DMT1) and colocalized with the cdy gene . We identified a nonsense mutation in the cdy allele and demonstrated that, whereas wild-type zebrafish DMT1 protein can transport iron, the truncated protein expressed in cdy mutants is not functional . Our studies further demonstrate the conservation of iron metabolism in vertebrates and suggest the existence of an alternative pathway of intestinal and red blood cell iron uptake. FEBS Lett, 2002 Oct 23, 530(1-3), 191 - 6 Physiological variation in metabolic phenotyping and functional genomic studies: use of orthogonal signal correction and PLS-DA; Gavaghan CL et al.; Metabolic phenotyping, or metabotyping, is increasingly being used as a probe in functional genomics studies . However, such profiling is subject to intrinsic physiological variation found in all animal populations . Using a nuclear magnetic resonance-based metabonomic approach, we show that diurnal variations in metabolism can obscure the interpretation of strain-related metabolic differences in two phenotypically normal mouse strains (C57BL10J and Alpk:ApfCD) . To overcome this problem, diurnal-related metabolic variation was removed from these spectral data by application of orthogonal signal correction (OSC), a data filtering method . Interpretation of the removed orthogonal variation indicated that diurnal-related variation had been removed and that the AM samples contained higher levels of creatine, hippurate, trimethylamine, succinate, citrate and 2-oxo-glutarate and lower levels of taurine, trimethylamine-N-oxide, spermine and 3-hydroxy-iso-valerate relative to the PM samples . We propose OSC will have great potential removing confounding variation obscuring subtle changes in metabolism in functional genomic studies and will be of benefit to optimising interpretation of proteomic and genomic datasets. Cancer Res, 2002 Oct 15, 62(20), 5818 - 27 Integrated functional genomics approach for the design of patient-individual antitumor vaccines; Weinschenk T et al.; Our aim is to identify as many candidates as possible for tumor-associated T-cell epitopes in individual patients . First, we performed expression profiling of tumor and normal tissue to identify genes exclusively expressed or overexpressed in the tumor sample . Then, using mass spectrometry, we characterized up to 77 different MHC ligands from the same tumor sample . Several of the MHC ligands were derived from overexpressed gene products, one was derived from a proto-oncogene, and another was derived from a frameshift mutation . At least one was identified as an actual T-cell epitope . Thus, we could show that by combining these two analytic tools, it is possible to propose several candidates for peptide-based immunotherapy . We envision the use of this novel integrated functional genomics approach for the design of antitumor vaccines tailored to suit the needs of each patient. Toxicol Appl Pharmacol, 2002 Sep 15, 183(3), 207 - 220 Defining the molecular and cellular basis of toxicity using comparative models; Ballatori N et al.; A critical element of any experimental design is the selection of the model that will be used to test the hypothesis . As Claude Bernard proposed over 100 years ago "the solution of a physiological or pathological problem often depends solely on the appropriate choice of the animal for the experiment so as to make the result clear and searching." Likewise, the Danish physiologist August Krogh in 1929 wrote that "For a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied." This scientific principle has been validated repeatedly in the intervening years as investigators have described unique models that exploit natural differences in chemical and molecular structure, biochemical function, or physiological response between different cells, tissues, and organisms to address specific hypotheses . Despite the power of this comparative approach, investigators have generally been reluctant to utilize nonmammalian or nonclassical experimental models to address questions of human biology . The perception has been that studies in relatively simple or evolutionarily ancient organisms would provide little insight into "complex" human biology . This perception, although always somewhat misguided, is now even less tenable given the results of the genome sequencing projects, which demonstrate that the human genome is remarkably similar to that of evolutionarily ancient organisms . Thus, the various life forms on Earth share much more in common then anyone had previously envisio